JGI Overview Now and the Future 9/02/09 · JGI Science & Operations Review. Dec 3 ‐ 5, 2008,...

Summary of the 2008 BER S&O Review– New JGI Management and Organizational

Structure– Changes in JGI Informatics

2009 JGI Five Year Strategic plan

JGI Overview Now and the Future9/02/09

JGI Science & Operations Review

Dec 3‐5, 2008, Report Issued March 3, 2009

• Science• Management• Operations• Informatics


Recent JGI Publication MetricsRecent JGI Publication Metrics

Total Peer-Reviewed Publications (Science/Nature/PNAS)

2009 citations of JGI- Authored Papers published 2005-Present

2009

81 (18)

18,919

Sorgum Genome Nature 2009

Two algal (Micromonas) Genome Science 2009

Sorgum Genome Nature 2009

Two algal (Micromonas) Genome Science 2009

Manuscripts in various stages of reviewGenomic Encyclopedia of Bacteria and Archea (under review Nature) Brachypodium Genome (submitted to Science)Soybean Genome (soon to be submitted)

JGI Operations and Management

• “Establish a centralized management and organizational structure”

• “Establish funding flow from LBNL to partners to align authority and responsibility”

ORNLHudson Alpha

(Stanford)

DOE-BER

LANL

JGI Director

• Coordination of JGI Scientific Goals Unlinked to Funding and Reporting

Walnut Creek

LBNL

LLNL


Metagenomics MicrobialFungal

Informatics

PlantOps/Ad

min

Dept Dir Bus. Ops, Inform., Prod.

Dept Dir Science Programs

JGI Director

DOE-BER

PNNL

HA

Reports/FWPsFunding

ORNL

LANLLANL

Production


JGIWalnut Creek

LANLH AH A

JGIWalnut Creek

JGIWalnut Creek

JGIWalnut Creek

• JGI Director Responsible and Accountable for JGI Productivity• Organization Broken into Programs• Programs Coordinate the JGI Scientific Goals Linked to Funding



JGI Director

PolicyBoardLBNL DirectorBER

S&OReview & Others

Science Advisory Board Joint CoordinatingCommittee

User Committee

Guidance & Oversight

Management Input

Guidance/Oversight & Management Input

(Science based programmatic funding decisions have already been made)

New Operations and Management Structure Progress

JGI Science Program Management Model Implemented

Science Program Leads Named and Functioning

Implemented Program Based Financial Planning & Reporting

“Remedy Senior Leadership Deficiencies”

Informatics

Concern about the Informatic Planning and Hardware Infrastructure Faced with

Dramatic Increases in Data Generation

Remedy Senior Leadership Deficiencies

JGI Informatics Department HeadJGI Informatics Department HeadSvilen Tzonev (Illumina / Solexa , Sr. Director of

Software Development and Bioinformatics)

JGI Chief Informatic Officer/ JGI Associate Director(New position)

Jill Mesirov Part Time Consultant to the JGI Director(CIO / Associate Director Broad Harvard MIT))

JGI Informatics Project Management Program Head(New position)

Evi Dube (Previously Computing Division Leader (LLNL))





Jill Mesirov Part Time Consultant to the JGI(CIO / Associate Director Broad Harvard MIT)

JGI Informatics Project Management Program Head(New position)






Jill Mesirov Part Time Consultant to the JGI Director(CIO / Associate Director Broad Harvard MIT))

JGI Informatics Project Manager(New position)


Informatics Advisory Committee (New advisory group)

First meeting scheduled Dec 09

Informatics

I. ARRA Funding Targeted for IT Upgrades: $11.1M

Funding Received-August 7th

Add Infrastructure for Management, Storage and Movement of Genome- Scale Datasets

Increase Storage (100% increase) Upgrade JGI’s Central Computing Cluster (200% increase)Upgrade ESNet Access

Concern about the JGI Informatic Infrastructure Faced with Dramatic Increases in Data Generation

Projects already underway or being developed

Using ScalaBLAST for Metagenomics

–

Porting ScalaBLAST to JGI clusters; help

parallelize short read assembler

Working with JGI on designing computing nodes

–

Scientific engagement with JGI on computational

challenges

–

IMG update using large BLAST runs focusing on

isolate genomes and potentially some of the new

Titanium metagenome datasets

–

Two large‐scale metagenomics problems

identified

•

Goal 1: evaluate metagenome assembly by using

simulated dataset

•

Goal 2 : evaluate gene calling through a large

blastx search against NR using joined Illumina

pair‐end reads.

–

Argonne team identified to assist JGI team

–

Assisted IMG in solving contentious

parallel computing bug

–

Working with JGI on designing computing

nodes

–

Possible Site for Remote Computing

II. Explore the DOE National Lab’s high performance computing capabilities to help JGI’s data intense challenges

Concern about the JGI Management Infrastructure Faced with Dramatic Increases in Data Generation

Informatics

Summary:Recruiting leadership to strategically as well as tactically chart the JGI’s informatic directions.

Additional informatic personnel and hardware.

Engaging the DOE National Labs to adapt their high performance computing capabilities to address JGI needs

Summary of S & O Review ResponseSummary of S & O Review Response

• 23 Committee Recommendations – Informatics (10 Recommendations)– Operations & Safety (7 Recommendations)– Science (4 Recommendations)– Management (2 Management)

• JGI Corrective Action Status – All Recommendations are either fully implemented or are in the

process of be implemented

• Corrective Action Milestones-Reviewed by JGI Senior Managers and Communicated with BER

DOE JGI 5DOE JGI 5--Year Strategic PlanYear Strategic Plan

Revolutionary Technological Changes

Sanger ,

Sanger , 454

Illumina

JGI 2004 Onward

Mission: User Facility for Large Scale Genomics and Analysis to Enable Bioenergy and Environmental Research

In carrying out genomics of focus, scale, and complexityUnique Capabilities

to help users solve important but hard DOE relevant problems

Plants, Microbes, Metagenomes User Facility

National Research Council Plant Genome Report 2008

“It is critical that JGI continue to serve a broad remit for sequencing and resequencing of plant genomes…”

Populus trichocarpa black cottonwoodChlamydomonas reinhardtii chlorophyte alga Physcomitrella patens bryophyte mossSorghum bicolor sorghumGlycine max soybeanPanicum virgatum switchgrassMiscanthus x giganteus miscanthusVolvox carteri multicellular green algaArabidopsis lyrata Lyrate rockcressSelaginella moellendorffii lycophyte fernBrachypodium distachyon false purple bromeMimulus guttatus monkeyflowerManihot esculenta cassavaPrunus persica peachSetaria italica foxtail milletCapsella rubella Pink Shepherd’s purseAquilegia coerulea Goldsmith columbine Gossypium raimondii diploid cottonEucalyptus grandis rose gumPhaseolus vulgaris Common beanZea mays (Mo17 inbred) maize

Plant Genomes

Flagship Plant Genomes (High Priority Organisms)

Sorghum Bicolor

Foxtail millet

Switchgrass

•Produce higher quality accurate and well annotated genomes•Add additional information

Brachypodium

Miscanthus

Chlamydomonas Poplar

Soybean

Problem with plant genomes:Though we have the sequence we

cannot assign function to most of it

Discovery of functional elements through

comparative genomics

JGI Pilot Project to Sequence and Analyze 12 Arabidopsis RelativJGI Pilot Project to Sequence and Analyze 12 Arabidopsis Relativeses (Project Leaders: Joe Ecker, Detlef Weigel, Dan Rokhsar)(Project Leaders: Joe Ecker, Detlef Weigel, Dan Rokhsar)

The 12 Arabidopsis Relatives Project will:

•Identify functional elements in these genomes based on evolutionary constraint

•Provide a road map for similar projects in plant groups with much larger genomese.g., grasses

The 12 Arabidopsis Relatives Project will:

•Identify functional elements in these genomes based on evolutionary constraint

•Provide a road map for similar projects in plant groups with much larger genomese.g., grasses

Goal of JGI Plant Program

Produce the genomic tools necessary to understand cell wall construction, feedstock production and carbon

sequestration and sunlight energy harvesting pathways

JGI Microbial Program:

Bacteria and Archaea 939 Complete Genomes (NCBI, August 2009)

JGI has produced ~30% of the world’s complete archaeal and bacterial genomes

3/4 of sequenced genomes belong to just three bacterial phyla

bacterial and archaeal phyla with cultured isolate



Gene AFxn A

Gene ?*Fxn?

Gene ?*Fxn?

Gene A*FxnA



Gene AFxn A

Gene?*Fxn?

Gene ?*Fxn?

Gene ?*Fxn?

Gene A*FxnA

Gene A*FxnA

Gene A*FxnA

“A phylogeny-based genomic encyclopedia of bacteria and archaea”(Final stage of Nature review)

H. Utahensis

(Final stages of Nature review)

“Significantly improves analysis of metagenomic data”

“Markedly improves the identification of new gene families and members of gene families”

including those of DOE relevance

Pilot Genomic Encyclopedia of Bacteria and ArchaeaGEBA (Sequencing and analysis of 64 genomes)

New Sequenced Phyla GEBA

H. Utahensis

27% NaCl Halorhabdus utahensis

6x saltier than ocean

Great Salt Lake

A cellulase gene cluster

Optimized Cellulases

DOE Bioenegy Center (JBEI)of Synthesized H Utahensis

Cellulases

High Salt Cellulase Activity

Ionic Liquid Detergents for Cellulose Dissolution

before after


Present State of Bacteria and Archaeal Genome Coverage(post GEBA)

The true extent of the coverage…. bacterial and archaeal diversity including major

uncultured phyla

Our ultimate goal…. bacterial and archaeal diversity including major uncultured phyla

5 m 5 m

Technologies for accessing the genomes of hard to culture organisms

JGI Fungal Program

WashU7%

Genoscope9%

JCVI5%

Broad Institute

27%

Other29%

JGI23%

Fungal genome projects worldwide

DegradeDegrade

Decomposers

Grow Grow

Plant symbionts and pathogens

Laccaria bicolor

FermentFerment

Pichia stipitis

Trichoderma reesei

http://philip9876.wordpress.com/2007/10/02/india-to-replace-10-per-cent-transport-fuels-with-biofuels-in-10-years/biofuel/

Vol.1. Plant feedstock healthPart 1. Mycorrhizal Symbionts (Basidiomycota) Part 2. Plant Pathogens (Dothideomycota)

Vol.2. Lignocellulose degradationWhite and brown rot (Basidiomycota)

Vol.3. FermentationVol.4. Industrial organisms

Part 1. Trichoderma spp. Part 2. Aspegillus nigri

\

Large Scale Genomic Analysis of Fungi

Genomic Encyclopedia of Fungi(GEF)

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http://rds.yahoo.com/_ylt=A0S020mEDotKHtoAUDujzbkF/SIG=12oq4qlik/EXP=1250713604/**http://www.bitkisagligi.net/Elma/elmaresim/Mycosphaerella_pomi-3.jpg

FossilNoonanScience

2004 2005 2006 20072008

Marine Archaeal Methane Oxidation

DeLong/PutnamScience

Acid Mine DrainageBanfield/Chapman

Nature

SoilTringe

Science

Olavius algarvensisDubilier/Woyke

Nature

Wastewater EBRHugenholtz

Nature Biotech

Marine PlanktonicDeLongScience

Termite GutLeadbetter/Hugenholtz

Nature

Oral TM7QuakePNAS

Deep MineChivianScience

JGI Metagenomics

2009

Lake WashingtonMethylotrophicChistoserdovaNature Biotech

recommended the establishment of a small number of large-scale projects to study particular habitats

Background for Metagenomics Plans

Soil Represents a habitat that is important due to its role in carbon and nitrogen cycling

and biomass production. It is a particularly “genomicaly” challenging environment due to its complexity.

Great Prairie Soil Metagenome Project

(Jim Tiedge, Phil Hugenholtz)

Multiple

Multiple samplings of 3 Different Prairie Sites

• Midwest prairie represents largest expanse of world’s most fertile soils

• Sequesters the most carbon of any soil system in the U.S.• Produces large amounts of biomass annually: Key for

biofuels, carbon sequestration

Iowa never-tilled prairie Iowa >100 yr tilled (corn)

Science drivers

• To improve soil management, carbon sequestration,

• Through genetic understanding maybe able to potentially manage traits such as green house gas fluxes, and carbon stability

How Do We hope to Use the Information:Great Prairie Soil Metagenome Project

Established Switchgrass (Wisconsin)

100,000 Great Prairie metagenomic project , ~100 Gbp

Termite hindgut, 62 Mbp62

1,000,000

Potential Future Projects:Terabase Projects

Increasing Scale of Metagenomic Projects in the Future

Terror terabase projects

Potential foci for 1Tb Grand Challenge

• Sequence the 12 Great Soil Orders (the major soil types)– Covers the extremes in soil diversity, e.g. permafrost to

tropical desert to alkali flats to taiga forest to wetlands

to discover gene adaptation to environmental

extremes.

Sequence the State Soil of each StateThese official state soils share the same distinction as

state flowers and birds.

JGI User Programs

JGI User Program Looking Forward

>1300 Usersbioenergy

carbon cyclingbiogeochemistry GTL and SFABRCs

BESC, GLBRC, JBEI

JGIUser facility for genome biology

High Performance ComputingProteomics Structural Biology

Single Cell Genomics

ResequencingGenomic Capture

ChIP-Seq

TranscriptomicsMapping

ANALYSIS

Opportunities and Challenges

55

Mining for biomass deconstruction enzymes

within the cow rumen

– Can introduce into the same cow nylon bags

containing different

Degradation of switchgrass in the rumen (72

hr incubation)

Pre

IncubationPost

Incubation

Opportunities from generating 18 GB of Data

Full Length Lignocellulolytic Genes

Bacteroides

Fibrobacteres

Gemmimonas

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Marine GroupAWS3

OP9

SynergistesDeferribacteres

Rumen project total size: ~18 GB

(Termite project total size: ~62 MB)

58

Challenge is the analysis of the 18 GB Cow

Rumen Data

~ 3 weeks on JGI’s1500-CPU-cluster

Computational bottleneck imminentTraditional analysis approaches won’t scalenew computational approaches needed

Focus on bringing National Lab computational infrastructure and expertise to bear on problems

associated with the volume and nature of next gen sequencer out-put

JGI-Sponsored Workshop on HPC for Next Gen Sequencing

Coupling the JGI’s data production with DOE Nat Lab HPC resources will advance energy and environmental science

It is not about the machines

JGI Overview Now and the Future 9/02/09 · JGI Science & Operations Review. Dec 3 ‐ 5, 2008,...

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